The mammalian SWI/SNF-like BAF complex is a 2-MDa ATP-dependent chromatin remodeler responsible for nucleosome clearance at the promoter regions of actively transcribed genes. The human BAF complex is composed of at least fifteen subunits, four of which have spatially and temporally restricted paralogues that function in targeting specificity through combinatorial assembly mechanisms. Perturbation of this assembly pathway through the alteration of key BAF subunits, as it is observed in approximately 20% cancers, is sufficient to cause gross compositional change of the residual complex and subsequent aberrant biological function. The oncogenic potential of BAF complex misassembly is most transparent in malignant rhabdoid tumor (MRT) and synovial sarcoma which are characterized by bi-allelic inactivation and translocation mutations, respectively. Both of these mutations result in the failure to incorporate BAF47 into the BAF complex. Using a proteomics approach, we have shown that the loss of BAF47 in MRT and synovial sarcoma results in compositionally distinct BAF complexes. These results are suggestive that BAF47 potentially functions as a keystone in combinatorial assembly through adjacent interactions with other BAF subunits. Furthermore, the presence of inactivating and truncation mutations in several other BAF subunits (e.g. BAF250A, BAF180, Brg1, and Brm) may also indicate a mutual dependency among other sets of BAF subunits. The full impact of these oncogenic mutations has yet to be elucidated due to the absence of a comprehensive BAF structure model and defined assembly pathway. To further our understanding of the consequences of BAF complex perturbation in cancer, I propose a strategic analysis of BAF complex structure by dissecting the BAF combinatorial assembly pathway using synovial sarcoma and MRT model systems. To accomplish this task, I aim to: (1) Define the BAF complex pathway of assembly through subunit dependencies, interfacial interactions, and subunit post-translational modifications, and (2) Investigate the differential targeting specificity of an array of altered complexes to understand the role of each subunit in BAF targeting. This seminal research will not only serve as a foundation in understanding compositional and specificity changes of the BAF complex that drive cancer, but also elucidate fundamental transcriptional control mechanisms that form a basis for complex signaling networks during growth and development. Furthermore, the culmination of these studies will serve as a platform for multiple drug discovery efforts through our collaboration with the Broad Institute.